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- PDB-3ddj: Crystal structure of a cbs domain-containing protein in complex w... -

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Basic information

Entry
Database: PDB / ID: 3ddj
TitleCrystal structure of a cbs domain-containing protein in complex with amp (sso3205) from sulfolobus solfataricus at 1.80 A resolution
ComponentsCBS domain-containing protein
KeywordsAMP-BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / CBS domain-containing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of CBS domain-containing protein in complex with AMP (NP_344512.1) from SULFOLOBUS SOLFATARICUS at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5333
Polymers34,0801
Non-polymers4532
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.560, 48.090, 83.280
Angle α, β, γ (deg.)90.000, 93.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CBS domain-containing protein


Mass: 34080.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: NP_344512.1, SSO3205 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97U20
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.76
Details: 23.0% polyethylene glycol 600, 0.1M phosphate-citrate pH 3.76, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→29.617 Å / Num. obs: 28983 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.648 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.860.5292.517350494893.2
1.86-1.940.3723.823077607099.4
1.94-2.030.2645.421827572499.5
2.03-2.130.1698.220249528999.6
2.13-2.270.11611.422873595599.7
2.27-2.440.0851521232552199.9
2.44-2.690.06319.322331579499.8
2.69-3.070.04326.721356552899.7
3.07-3.870.02837.622222574599.9
3.870.02345.322172570899.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDAUTOSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.617 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.781 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. PEG (PEG600) IS PRESENT IN CRYSTALLIZATION CONDITION. 5. AMP WAS MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1469 5.1 %RANDOM
Rwork0.168 ---
obs0.17 28971 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.676 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-0.98 Å2
2--1.87 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 30 283 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222306
X-RAY DIFFRACTIONr_bond_other_d0.0010.021553
X-RAY DIFFRACTIONr_angle_refined_deg1.5092.0013141
X-RAY DIFFRACTIONr_angle_other_deg0.9733837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59324.56592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29515434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7121514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022486
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.2040.2481
X-RAY DIFFRACTIONr_nbd_other0.190.21699
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21161
X-RAY DIFFRACTIONr_nbtor_other0.0870.21198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.221
X-RAY DIFFRACTIONr_mcbond_it2.25931550
X-RAY DIFFRACTIONr_mcbond_other0.5453571
X-RAY DIFFRACTIONr_mcangle_it2.99552335
X-RAY DIFFRACTIONr_scbond_it4.8078957
X-RAY DIFFRACTIONr_scangle_it6.62611796
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 101 -
Rwork0.226 1889 -
all-1990 -
obs--93.03 %
Refinement TLS params.Method: refined / Origin x: 8.5137 Å / Origin y: 20.2633 Å / Origin z: -20.4589 Å
111213212223313233
T-0.0468 Å20.0168 Å20.0047 Å2--0.0597 Å2-0.0052 Å2---0.0518 Å2
L1.231 °20.0239 °20.485 °2-0.2227 °20.0421 °2--1.1451 °2
S-0.0185 Å °0.0173 Å °0.0387 Å °-0.0145 Å °0.0117 Å °0.0189 Å °-0.0289 Å °0.0025 Å °0.0068 Å °

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